LAUSR

Background Prisons are high-risk settings for infectious disease outbreaks due to their highly dynamic and crowded nature. During late 2020, prisons in England observed a surge in COVID-19 infection. This study describes the emergence of the Alpha variant in prisons during this period. Methods Alpha and non-Alpha variant COVID-19 cases were identified in prisoners in England using address-matched laboratory notifications and genomic information from COG-UK. Results Of 14,094 COVID-19 positive prisoner cases between 1st October 2020 – 28th March 2021, 11.5% (n=1,621) had sequencing results. Of these, 1,082 (66.7%) were identified as the Alpha variant. 29 (2.7%) Alpha cases required hospitalisation compared to only 5 (1.0%; p=0.02) non-Alpha cases. A total of 14 outbreaks were identified with the median attack rate higher for Alpha (17.9%, IQR 3.2% - 32.2%; p=0.11) than non-Alpha outbreaks (3.5%, IQR 2.0% - 10.2%). Conclusion Higher attack rates and increased likelihood of hospitalisations were observed for Alpha cases compared to non-Alpha. This suggests a key contribution to the rise in cases, hospitalisations and outbreaks in prisons in the second wave. With prisons prone to COVID-19 outbreaks, and the potential to act as reservoirs for variants of concern, sequencing of prison-associated cases alongside whole-institution vaccination should be prioritised.